1a9j: Difference between revisions

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[[Image:1a9j.gif|left|200px]]


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==APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTURE==
The line below this paragraph, containing "STRUCTURE_1a9j", creates the "Structure Box" on the page.
<StructureSection load='1a9j' size='340' side='right'caption='[[1a9j]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1a9j]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A9J FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
{{STRUCTURE_1a9j|  PDB=1a9j  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1a9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a9j OCA], [https://pdbe.org/1a9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a9j RCSB], [https://www.ebi.ac.uk/pdbsum/1a9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a9j ProSAT]</span></td></tr>
 
</table>
'''APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTURE'''
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</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Beger RD]]
Natural and exogenous processes can give rise to abasic sites with either a purine or pyrimidine as the base on the opposing strand. The solution state structures of the apyrimidinic DNA duplex, with D6 indicating an abasic site, [sequence: see text] referred to as AD, and the apurinic DNA duplex with a dC17, referred to as CD, have been determined. A particularly striking difference is that the abasic site in CD is predominantly a beta hemiacetal, whereas in AD the alpha and beta forms are equally present. Hydrogen bonding with water by the abasic site and the base on the opposite strand appears to play a large role in determining the structure near the damaged site. Comparison of these structures with that of a duplex DNA containing a thymine glycol at the same position as the abasic site and with that of a duplex DNA containing an abasic site in the middle of a curved DNA sequence offers some insight into the common and distinct structural features of damaged DNA sites.
[[Category: Bolton PH]]
 
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A9J OCA].  
 
==Reference==
Structures of apurinic and apyrimidinic sites in duplex DNAs., Beger RD, Bolton PH, J Biol Chem. 1998 Jun 19;273(25):15565-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9624147 9624147]
[[Category: Beger, R D.]]
[[Category: Bolton, P H.]]
[[Category: Apyrimidinic dna]]
[[Category: Damaged dna]]
[[Category: Water]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:01:00 2008''

Latest revision as of 11:05, 10 April 2024

APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTUREAPYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTURE

Structural highlights

1a9j is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
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